Add support for compressed handles

src/main/java/org/scijava/io/handle/BZip2Handle.java

@@ -0,0 +1,64 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io.handle;
+
+import java.io.IOException;
+
+import org.scijava.io.handle.bzip2.CBZip2InputStream;
+import org.scijava.io.location.AbstractCompressedHandle;
+import org.scijava.io.location.BZip2Location;
+import org.scijava.plugin.Plugin;
+
+/**
+ * {@link DataHandle} for a {@link BZip2Location}.
+ *
+ * @author Gabriel Einsdorf
+ */
+@Plugin(type = DataHandle.class)
+public class BZip2Handle extends AbstractCompressedHandle<BZip2Location> {
+
+	@Override
+	protected void initInputStream() throws IOException {
+
+		int skipped = 0;
+		// ensure 2 bytes are skipped
+		while (skipped < 2) {
+			skipped += raw().skip(2l - skipped);
+		}
+		inputStream = new CBZip2InputStream(raw(), log());
+	}
+
+	@Override
+	public Class<BZip2Location> getType() {
+		return BZip2Location.class;
+	}
+}

src/main/java/org/scijava/io/handle/BufferedStreamHandle.java

@@ -0,0 +1,45 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io.handle;
+
+import org.scijava.io.location.Location;
+
+/**
+ * A buffered {@link StreamHandle}.
+ * 
+ * @author Gabriel Einsdorf
+ */
+public interface BufferedStreamHandle<L extends Location> extends
+	SeekableStreamHandle<L>
+{
+
+}

src/main/java/org/scijava/io/handle/DefaultBufferedStreamHandle.java

@@ -0,0 +1,239 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io.handle;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.scijava.io.ByteArrayByteBank;
+import org.scijava.io.ByteBank;
+import org.scijava.io.location.Location;
+
+/**
+ * A {@link BufferedStreamHandle} backed by a {@link ByteBank}.
+ * 
+ * @author Gabriel Einsdorf
+ */
+public class DefaultBufferedStreamHandle<L extends Location> extends
+	AbstractStreamHandle<L> implements BufferedStreamHandle<L>
+{
+
+	private static final int CHUNK_SIZE = 8192;
+
+	private final StreamHandle<L> handle;
+	private ByteBank buffer;
+
+	private InputStream inStreamProxy;
+	private OutputStream outStreamProxy;
+
+	private boolean closed;
+
+	/**
+	 * Wraps around StreamHandle in a buffer
+	 *
+	 * @param handle
+	 */
+	public DefaultBufferedStreamHandle(final StreamHandle<L> handle) {
+		this.handle = handle;
+	}
+
+	@Override
+	public byte readByte() throws IOException {
+
+		// reached end of the buffer
+		if (offset() == handle.length()) {
+			return -1;
+		}
+
+		// check if we need to refill the buffer
+		if (offset() > maxBuf() || maxBuf() == -1) {
+			// buffer more bytes
+			final int filled = fill();
+			if (filled <= 0) {
+				// no more bytes in input handle
+				return -1;
+			}
+		}
+
+		byte b = getBufferIfOpen().getByte(offset());
+		advance(1);
+		return b;
+	}
+
+	@Override
+	public void seek(final long pos) throws IOException {
+		final long off = offset();
+		if (off == pos) return;
+		if (pos > off) {
+			// ensure target is buffered
+			while (pos > maxBuf()) {
+				fill();
+			}
+		}
+		// values in the range (pos < off) are already buffered
+		setOffset(pos);
+	}
+
+	private long maxBuf() throws IOException {
+		return getBufferIfOpen().size() - 1;
+	}
+
+	@Override
+	public long skip(final long n) throws IOException {
+		seek(offset() + n);
+		return handle().skip(n);
+	}
+
+	@Override
+	public int read(final byte[] b, final int off, final int len)
+		throws IOException
+	{
+
+		while (maxBuf() < offset() + len) {
+			final int filled = fill();
+			if (filled <= 0) {
+				// no more bytes available
+				break;
+			}
+		}
+
+		// read all available bytes
+		int available = (int) available(len);
+		getBufferIfOpen().getBytes(offset(), b, off, available);
+		setOffset(offset() + available);
+		return available;
+	}
+
+	/**
+	 * Fills the buffer with XX more bytes
+	 *
+	 * @throws IOException
+	 */
+	private int fill() throws IOException {
+		final byte[] buf = new byte[CHUNK_SIZE];
+		final int read = handle().read(buf);
+		if (read <= 0) {
+			return -1;
+		}
+		getBufferIfOpen().appendBytes(buf, read);
+		return read;
+	}
+
+	@Override
+	public InputStream in() {
+		if (inStreamProxy == null) {
+			inStreamProxy = new DataHandleInputStream<>(this);
+		}
+		return inStreamProxy;
+	}
+
+	@Override
+	public OutputStream out() {
+		if (outStreamProxy == null) {
+			outStreamProxy = new DataHandleOutputStream<>(this);
+		}
+		return outStreamProxy;
+	}
+
+	@Override
+	public long length() throws IOException {
+		return handle().length();
+	}
+
+	private StreamHandle<L> handle() throws IOException {
+		if (closed) {
+			throw new IOException("Handle is closed!");
+		}
+		return handle;
+	}
+
+	@Override
+	public void setLength(final long length) throws IOException {
+		handle().setLength(length);
+	}
+
+	@Override
+	public boolean isReadable() {
+		return !closed && handle.isReadable();
+	}
+
+	@Override
+	public boolean isWritable() {
+		return !closed && handle.isWritable();
+	}
+
+	@Override
+	public boolean exists() throws IOException {
+		return handle.exists();
+	}
+
+	@Override
+	public Class<L> getType() {
+		return handle.getType();
+	}
+
+	@Override
+	public void resetStream() throws IOException {
+		getBufferIfOpen();
+		if (handle() instanceof ResettableStreamHandle) {
+			((ResettableStreamHandle<L>) handle()).resetStream();
+		}
+		else {
+			throw new IOException("Handle can not be reset!");
+		}
+	}
+
+	@Override
+	public void close() throws IOException {
+		if (!closed) {
+			closed = true;
+			handle().close();
+			getBufferIfOpen().clear();
+			buffer = null;
+		}
+	}
+
+	/**
+	 * @return the buffer used in this handle
+	 * @throws IOException if this handle has been closed
+	 */
+	private ByteBank getBufferIfOpen() throws IOException {
+		if (closed) {
+			throw new IOException("Handle is closed");
+		}
+		if (buffer == null) {
+			buffer = new ByteArrayByteBank();
+		}
+		return buffer;
+	}
+}